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Fix: "invalid pod status" when running scrips with the kubernetes executor. #1242

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merged 5 commits into from Jul 23, 2019
Merged

Fix: "invalid pod status" when running scrips with the kubernetes executor. #1242

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157ef34
Fixes "invalid pod status" error when container status is missing in …
Jul 22, 2019
c93df5a
Test for missing container condition from the kubernetes api.
Jul 22, 2019
2d74314
Updated K8sResponseException message to be clearer about why it was t…
Jul 23, 2019
7a96e12
Updated K8sResponseException message.
Jul 23, 2019
f638a19
Updated tests to reflect new K8sResponseException text.
Jul 23, 2019
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20 changes: 11 additions & 9 deletions modules/nextflow/src/main/groovy/nextflow/k8s/client/K8sClient.groovy
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Expand Up @@ -244,20 +244,22 @@ class K8sClient {
return state
}

if( status?.phase == 'Pending' && status.conditions instanceof List ) {
final allConditions = status.conditions as List<Map>
final cond = allConditions.find { cond -> cond.type == 'PodScheduled' }
if( cond.reason == 'Unschedulable' ) {
def message = "K8s pod cannot be scheduled"
if( cond.message ) message += " -- $cond.message"
//def cause = new K8sResponseException(resp)
log.warn1(message)
if( status?.phase == 'Pending' ){
if( status.conditions instanceof List ) {
final allConditions = status.conditions as List<Map>
final cond = allConditions.find { cond -> cond.type == 'PodScheduled' }
if( cond.reason == 'Unschedulable' ) {
def message = "K8s pod cannot be scheduled"
if( cond.message ) message += " -- $cond.message"
//def cause = new K8sResponseException(resp)
log.warn1(message)
}
}
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// undetermined status -- return an empty response
return Collections.emptyMap()
}

throw new K8sResponseException("K8s invalid pod status (missing container status)", resp)
throw new K8sResponseException("K8s undetermined status conditions for pod $podName", resp)
}
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Frankly, I think the previous err message was a bit more informative.

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@olifly olifly Jul 23, 2019 •
edited

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@pditommaso The previous message did not reflect why the Exception was being thrown anymore. The problem is not missing container status, but rather that K8s returned a set of phase and conditions that the code can not determine the pod state (end of function without any resolvement).

I can revert the change to the message, or insert a more informative message of your choice 😄 (I'm really bad at constructing error message btw 🙈)

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Fair enough, what about K8s undermined status conditions for pod $podName ?

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Fair enough, what about K8s undermined status conditions for pod $podName ?

Sounds good to me. Will update pull request.


protected void checkInvalidWaitingState( Map waiting, K8sResponseJson resp ) {
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44 changes: 42 additions & 2 deletions modules/nextflow/src/test/groovy/nextflow/k8s/client/K8sClientTest.groovy
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Expand Up @@ -426,6 +426,46 @@ class K8sClientTest extends Specification {
result == [:]
}

def 'should return undetermined status when status conditions are missing' () {
given:
def JSON = '''
{
"kind": "Pod",
"apiVersion": "v1",
"metadata": {
"name": "nf-89b34d7c2d1dc11daad72b1fcf7e0540",
"namespace": "default",
"selfLink": "/api/v1/namespaces/default/pods/nf-89b34d7c2d1dc11daad72b1fcf7e0540/status",
"uid": "02c3a34d-7720-11e9-8e1a-0a8b849038f8",
"resourceVersion": "21753960",
"creationTimestamp": "2019-05-15T14:44:58Z",
"labels": {
"app": "nextflow",
"processName": "split_input_file",
"runName": "hopeful_lalande",
"sessionId": "uuid-6b10c771-1a70-4af0-92be-7c0280e0e17f",
"taskName": "split_input_file_variants.gord_chr11_72000001-78000000",
}
},

"status": {
"phase": "Pending",
"qosClass": "Guaranteed"
}
}
'''

def client = Spy(K8sClient)
final POD_NAME = 'nf-89b34d7c2d1dc11daad72b1fcf7e0540'

when:
def result = client.podState(POD_NAME)
then:
1 * client.podStatus(POD_NAME) >> new K8sResponseJson(JSON)

result == [:]
}

def 'should fail to get pod state' () {

given:
Expand All @@ -439,14 +479,14 @@ class K8sClientTest extends Specification {
then:
1 * client.podStatus(POD_NAME) >> new K8sResponseJson([:])
e = thrown(K8sResponseException)
e.message.startsWith('K8s invalid pod status (missing container status)')
e.message.startsWith('K8s undetermined status conditions for pod')

when:
client.podState(POD_NAME)
then:
1 * client.podStatus(POD_NAME) >> new K8sResponseJson([status:[containerStatuses: []]])
e = thrown(K8sResponseException)
e.message.startsWith('K8s invalid pod status (missing container status)')
e.message.startsWith('K8s undetermined status conditions for pod')

when:
client.podState(POD_NAME)
Expand Down